[2023-06-05 14:49:02,481] [INFO] DFAST_QC pipeline started.
[2023-06-05 14:49:02,483] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 14:49:02,483] [INFO] DQC Reference Directory: /var/lib/cwl/stgdb5b1206-2b31-4efa-b231-dfae7712b42f/dqc_reference
[2023-06-05 14:49:03,703] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 14:49:03,704] [INFO] Task started: Prodigal
[2023-06-05 14:49:03,704] [INFO] Running command: gunzip -c /var/lib/cwl/stg597a4012-b7f2-4350-8f03-58b841ed5725/GCA_934486765.1_ERR7738580_bin.174_genomic.fna.gz | prodigal -d GCA_934486765.1_ERR7738580_bin.174_genomic.fna/cds.fna -a GCA_934486765.1_ERR7738580_bin.174_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 14:49:07,527] [INFO] Task succeeded: Prodigal
[2023-06-05 14:49:07,527] [INFO] Task started: HMMsearch
[2023-06-05 14:49:07,528] [INFO] Running command: hmmsearch --tblout GCA_934486765.1_ERR7738580_bin.174_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdb5b1206-2b31-4efa-b231-dfae7712b42f/dqc_reference/reference_markers.hmm GCA_934486765.1_ERR7738580_bin.174_genomic.fna/protein.faa > /dev/null
[2023-06-05 14:49:07,795] [INFO] Task succeeded: HMMsearch
[2023-06-05 14:49:07,796] [INFO] Found 6/6 markers.
[2023-06-05 14:49:07,819] [INFO] Query marker FASTA was written to GCA_934486765.1_ERR7738580_bin.174_genomic.fna/markers.fasta
[2023-06-05 14:49:07,819] [INFO] Task started: Blastn
[2023-06-05 14:49:07,820] [INFO] Running command: blastn -query GCA_934486765.1_ERR7738580_bin.174_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb5b1206-2b31-4efa-b231-dfae7712b42f/dqc_reference/reference_markers.fasta -out GCA_934486765.1_ERR7738580_bin.174_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 14:49:08,443] [INFO] Task succeeded: Blastn
[2023-06-05 14:49:08,447] [INFO] Selected 15 target genomes.
[2023-06-05 14:49:08,447] [INFO] Target genome list was writen to GCA_934486765.1_ERR7738580_bin.174_genomic.fna/target_genomes.txt
[2023-06-05 14:49:08,451] [INFO] Task started: fastANI
[2023-06-05 14:49:08,451] [INFO] Running command: fastANI --query /var/lib/cwl/stg597a4012-b7f2-4350-8f03-58b841ed5725/GCA_934486765.1_ERR7738580_bin.174_genomic.fna.gz --refList GCA_934486765.1_ERR7738580_bin.174_genomic.fna/target_genomes.txt --output GCA_934486765.1_ERR7738580_bin.174_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 14:49:15,708] [INFO] Task succeeded: fastANI
[2023-06-05 14:49:15,708] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdb5b1206-2b31-4efa-b231-dfae7712b42f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 14:49:15,708] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdb5b1206-2b31-4efa-b231-dfae7712b42f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 14:49:15,710] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 14:49:15,710] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 14:49:15,710] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-06-05 14:49:15,712] [INFO] DFAST Taxonomy check result was written to GCA_934486765.1_ERR7738580_bin.174_genomic.fna/tc_result.tsv
[2023-06-05 14:49:15,713] [INFO] ===== Taxonomy check completed =====
[2023-06-05 14:49:15,713] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 14:49:15,713] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdb5b1206-2b31-4efa-b231-dfae7712b42f/dqc_reference/checkm_data
[2023-06-05 14:49:15,716] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 14:49:15,740] [INFO] Task started: CheckM
[2023-06-05 14:49:15,740] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934486765.1_ERR7738580_bin.174_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934486765.1_ERR7738580_bin.174_genomic.fna/checkm_input GCA_934486765.1_ERR7738580_bin.174_genomic.fna/checkm_result
[2023-06-05 14:49:34,230] [INFO] Task succeeded: CheckM
[2023-06-05 14:49:34,231] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 14:49:34,256] [INFO] ===== Completeness check finished =====
[2023-06-05 14:49:34,257] [INFO] ===== Start GTDB Search =====
[2023-06-05 14:49:34,257] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934486765.1_ERR7738580_bin.174_genomic.fna/markers.fasta)
[2023-06-05 14:49:34,257] [INFO] Task started: Blastn
[2023-06-05 14:49:34,258] [INFO] Running command: blastn -query GCA_934486765.1_ERR7738580_bin.174_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb5b1206-2b31-4efa-b231-dfae7712b42f/dqc_reference/reference_markers_gtdb.fasta -out GCA_934486765.1_ERR7738580_bin.174_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 14:49:35,269] [INFO] Task succeeded: Blastn
[2023-06-05 14:49:35,274] [INFO] Selected 11 target genomes.
[2023-06-05 14:49:35,274] [INFO] Target genome list was writen to GCA_934486765.1_ERR7738580_bin.174_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 14:49:35,279] [INFO] Task started: fastANI
[2023-06-05 14:49:35,280] [INFO] Running command: fastANI --query /var/lib/cwl/stg597a4012-b7f2-4350-8f03-58b841ed5725/GCA_934486765.1_ERR7738580_bin.174_genomic.fna.gz --refList GCA_934486765.1_ERR7738580_bin.174_genomic.fna/target_genomes_gtdb.txt --output GCA_934486765.1_ERR7738580_bin.174_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 14:49:39,531] [INFO] Task succeeded: fastANI
[2023-06-05 14:49:39,550] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 14:49:39,550] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_900543215.1	s__UBA737 sp900543215	96.7233	442	580	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA737	95.0	97.02	96.96	0.84	0.79	3	conclusive
GCA_002451855.1	s__UBA737 sp002451855	94.2948	401	580	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA737	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017391425.1	s__UBA737 sp017391425	85.6319	368	580	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA737	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002431945.1	s__UBA737 sp002431945	81.1237	335	580	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA737	95.0	97.08	96.44	0.77	0.66	6	-
GCA_900547305.1	s__UBA737 sp900547305	80.0316	248	580	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA737	95.0	99.91	99.91	0.93	0.93	2	-
GCA_900549055.1	s__UBA737 sp900549055	80.0024	205	580	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA737	95.0	97.22	96.30	0.81	0.81	4	-
GCA_905193585.1	s__UBA737 sp905193585	79.9236	202	580	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA737	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549755.1	s__UBA737 sp900549755	79.9103	225	580	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA737	95.0	97.98	97.93	0.82	0.76	3	-
GCA_900547445.1	s__UBA737 sp900547445	78.9859	189	580	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA737	95.0	99.98	99.98	0.91	0.91	2	-
GCA_016302625.1	s__UBA737 sp016302625	78.1169	149	580	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA737	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 14:49:39,553] [INFO] GTDB search result was written to GCA_934486765.1_ERR7738580_bin.174_genomic.fna/result_gtdb.tsv
[2023-06-05 14:49:39,554] [INFO] ===== GTDB Search completed =====
[2023-06-05 14:49:39,558] [INFO] DFAST_QC result json was written to GCA_934486765.1_ERR7738580_bin.174_genomic.fna/dqc_result.json
[2023-06-05 14:49:39,558] [INFO] DFAST_QC completed!
[2023-06-05 14:49:39,558] [INFO] Total running time: 0h0m37s